logs: migrate to molecular CoT JSON protocol, fix regressions

- Replace BeliefFormatter with CotJsonFormatter (single-line JSON with
  ts, level, trace_id, src, marker, intent, payload, error, span_id)
- Migrate belief_scope to use cot_log() for structured JSON output
- Update monkey-patched reason/reflect/explore to pass extra= dict
- Strip 200+ inline [REASON]/[REFLECT]/[EXPLORE] markers from 50+ files
- Remove belief_scope from hot-path utilities (_parse_datetime,
  _json_load_if_needed) to eliminate startup log noise
- Register TraceContextMiddleware in app.py (was implemented but unused)
- Seed trace_id in startup_event/shutdown_event for background tasks
- Fix broken relative imports in translate routes (3 dots → 4 dots)
- Migrate 43 translate_routes log calls to logger.reason/explore
- Fix SyntaxError (positional arg after extra=) in _repo_operations_routes
- Fix IndentationError in rbac_permission_catalog except-block
- Add smoke test tests/test_smoke_app.py (catches import errors before run)

backend/src/api/routes/git/_helpers.py

@@ -61,8 +61,9 @@ def _resolve_repository_status(dashboard_id: int) -> dict:
     git_service = get_git_service()
     repo_path = git_service._get_repo_path(dashboard_id)
     if not os.path.exists(repo_path):
-        logger.debug(
-            f"[get_repository_status][REASON] Repository is not initialized for dashboard {dashboard_id}"
+        logger.reason(
+            f"Repository is not initialized for dashboard {dashboard_id}",
+            extra={"src": "get_repository_status"},
         )
         return _build_no_repo_status_payload()
 
@@ -70,8 +71,9 @@ def _resolve_repository_status(dashboard_id: int) -> dict:
         return git_service.get_status(dashboard_id)
     except HTTPException as e:
         if e.status_code == 404:
-            logger.debug(
-                f"[get_repository_status][REASON] Repository is not initialized for dashboard {dashboard_id}"
+            logger.reason(
+                f"Repository is not initialized for dashboard {dashboard_id}",
+                extra={"src": "get_repository_status"},
             )
             return _build_no_repo_status_payload()
         raise
@@ -287,10 +289,9 @@ def _resolve_current_user_git_identity(
             .first()
         )
     except Exception as resolve_error:
-        logger.warning(
-            "[_resolve_current_user_git_identity][REASON] Failed to load profile preference for user %s: %s",
-            user_id,
-            resolve_error,
+        logger.explore(
+            "Failed to load profile preference for resolving git identity",
+            extra={"src": "_resolve_current_user_git_identity", "payload": {"user_id": user_id}, "error": str(resolve_error)},
         )
         return None
 

backend/src/api/routes/git/_repo_operations_routes.py

@@ -128,23 +128,17 @@ async def pull_changes(
                         config_url = config_row.url
                         config_provider = config_row.provider
             except Exception as diagnostics_error:
-                logger.warning(
-                    "[pull_changes][REASON] Failed to load repository binding diagnostics for dashboard %s: %s",
-                    dashboard_id,
-                    diagnostics_error,
+                logger.explore(
+                    "Failed to load repository binding diagnostics",
+                    extra={"src": "pull_changes", "payload": {"dashboard_id": dashboard_id}, "error": str(diagnostics_error)},
                 )
-            logger.info(
-                "[pull_changes][REASON] Route diagnostics dashboard_ref=%s env_id=%s resolved_dashboard_id=%s "
-                "binding_exists=%s binding_local_path=%s binding_remote_url=%s binding_config_id=%s config_provider=%s config_url=%s",
-                dashboard_ref,
-                env_id,
-                dashboard_id,
-                bool(db_repo),
-                (db_repo.local_path if db_repo else None),
-                (db_repo.remote_url if db_repo else None),
-                (db_repo.config_id if db_repo else None),
-                config_provider,
-                config_url,
+            logger.reason(
+                f"Route diagnostics dashboard_ref={dashboard_ref} env_id={env_id} resolved_dashboard_id={dashboard_id} "
+                f"binding_exists={bool(db_repo)} binding_local_path={(db_repo.local_path if db_repo else None)} "
+                f"binding_remote_url={(db_repo.remote_url if db_repo else None)} "
+                f"binding_config_id={(db_repo.config_id if db_repo else None)} "
+                f"config_provider={config_provider} config_url={config_url}",
+                extra={"src": "pull_changes"},
             )
             _apply_git_identity_from_profile(dashboard_id, db, current_user)
             _gs.pull_changes(dashboard_id)
@@ -190,10 +184,9 @@ async def get_repository_status_batch(
     with belief_scope("get_repository_status_batch"):
         dashboard_ids = list(dict.fromkeys(request.dashboard_ids))
         if len(dashboard_ids) > MAX_REPOSITORY_STATUS_BATCH:
-            logger.warning(
-                "[get_repository_status_batch][REASON] Batch size %s exceeds limit %s. Truncating request.",
-                len(dashboard_ids),
-                MAX_REPOSITORY_STATUS_BATCH,
+            logger.reason(
+                f"Batch size {len(dashboard_ids)} exceeds limit {MAX_REPOSITORY_STATUS_BATCH}. Truncating request.",
+                extra={"src": "get_repository_status_batch"},
             )
             dashboard_ids = dashboard_ids[:MAX_REPOSITORY_STATUS_BATCH]
 

backend/src/api/routes/git/_repo_routes.py

@@ -61,8 +61,9 @@ async def init_repository(
             raise HTTPException(status_code=404, detail="Git configuration not found")
 
         try:
-            logger.info(
-                f"[init_repository][REASON] Initializing repo for dashboard {dashboard_id}"
+            logger.reason(
+                f"Initializing repo for dashboard {dashboard_id}",
+                extra={"src": "init_repository"},
             )
             _gs.init_repo(
                 dashboard_id,